Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.

Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer.

Extracellular microbe-mineral electron transfer is a major driving force for the oxidation of organic carbon in many subsurface environments. Extracellular multi-heme cytochromes of the Shewenella genus play a major role in this process but the mechanism of electron exchange at the interface between cytochrome and acceptor is widely debated. The 1.8 Å x-ray crystal structure of the decaheme MtrC revealed a highly conserved CX8C disulfide that, when substituted for AX8A, severely compromised the ability of S. oneidensis to grow under aerobic conditions. Reductive cleavage of the disulfide in the presence of flavin mononucleotide (FMN) resulted in the reversible formation of a stable flavocytochrome. Similar results were also observed with other decaheme cytochromes, OmcA, MtrF and UndA. The data suggest that these decaheme cytochromes can transition between highly reactive flavocytochromes or less reactive cytochromes, and that this transition is controlled by a redox active disulfide that responds to the presence of oxygen.

The crystal structure of the extracellular 11-heme cytochrome UndA reveals a conserved 10-heme motif and defined binding site for soluble iron chelates.

Members of the genus Shewanella translocate deca- or undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/egress sites arranged within four domains. Sequence and structural alignment of UndA and the deca-heme MtrF reveals the extra heme of UndA is inserted between MtrF hemes 6 and 7. The remaining UndA hemes can be superposed over the heme chain of the decaheme MtrF, suggesting that a ten heme core is conserved between outer membrane cytochromes. The UndA structure has also been crystallographically resolved in complex with substrates, an Fe(III)-nitrilotriacetate dimer or an Fe(III)-citrate trimer. The structural resolution of these UndA-Fe(III)-chelate complexes provides a rationale for previous kinetic measurements on UndA and other outer membrane cytochromes.

Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions.

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.

Quantitative 3-D elemental mapping by LA-ICP-MS of a basaltic clast from the Hanford 300 Area, Washington, USA.

Laser ablation with inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to measure elemental concentrations at the 100-µm scale in a 3-dimensional manner within a basaltic clast sample collected from the Hanford 300 Area in south-central Washington State, United States. A calibration method was developed to quantify the LA-ICP-MS signal response using a constant-sum mass fraction of eight major elements; the method produced reasonable concentration measurements for both major and trace elements when compared to a standard basalt sample with known concentrations. 3-Dimensional maps (stacked 2-D contour layers, each representing 2100 µm × 2100 µm) show relatively uniform concentration with depth for intrinsic elements such as Si, Na, and Sr. However, U and Cu accumulation were observed near the sample surface, consistent with the site's release history of these contaminants. U and Cu show substantial heterogeneity in their concentration distributions within horizontal slices, while the intrinsic elements are essentially uniformly distributed. From these measured U concentrations and published grain size distributions, gravel and cobbles were estimated to contain about 1% of the contaminant U, implicating the coarse fraction as a long-term release source.

Structure of a bacterial cell surface decaheme electron conduit.

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split ß-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.

The role of multihaem cytochromes in the respiration of nitrite in Escherichia coli and Fe(III) in Shewanella oneidensis.

The periplasmic nitrite reductase system from Escherichia coli and the extracellular Fe(III) reductase system from Shewanella oneidensis contain multihaem c-type cytochromes as electron carriers and terminal reductases. The position and orientation of the haem cofactors in multihaem cytochromes from different bacteria often show significant conservation despite different arrangements of the polypeptide chain. We propose that the decahaem cytochromes of the iron reductase system MtrA, MtrC and OmcA comprise pentahaem 'modules' similar to the electron donor protein, NrfB, from E. coli. To demonstrate this, we have isolated and characterized the N-terminal pentahaem module of MtrA by preparing a truncated form containing five covalently attached haems. UV-visible spectroscopy indicated that all five haems were low-spin, consistent with the presence of bis-His ligand co-ordination as found in full-length MtrA.

Biostimulation of iron reduction and subsequent oxidation of sediment containing Fe-silicates and Fe-oxides: effect of redox cycling on Fe(III) bioreduction.

Sediment containing a mixture of iron (Fe)-phases, including Fe-oxides (mostly Al-goethite) and Fe-silicates (illites and vermiculite) was bioreduced in a long-term flow through column experiment followed by re-oxidation with dissolved oxygen. The objective of this study was (a) to determine the nature of the re-oxidized Fe(III), and (b) to determine how redox cycling of Fe would affect subsequent Fe(III)-bioavailability. In addition, the effect of Mn on Fe(III) reduction was explored.(57)Fe-Mössbauer spectroscopy measurements showed that biostimulation resulted in partial reduction (20%) of silicate Fe(III) to silicate Fe(II) while the reduction of goethite was negligible. Furthermore, the reduction of Fe in the sediment was uniform throughout the column. When, after biostimulation, 3900 pore volumes of a solution containing dissolved oxygen was pumped through the column over a period of 81 days, approximately 46% of the reduced silicate Fe(II) was re-oxidized to silicate Fe(III). The Mössbauer spectra of the re-oxidized sample were similar to that of pristine sediment implying that Fe-mineralogy of the re-oxidized sediment was mineralogically similar to that of the pristine sediment. In accordance to this, batch experiments showed that Fe(III) reduction occurred at a similar rate although time until Fe(II) buildup started was longer in the pristine sediment than re-oxidized sediment under identical seeding conditions. This was attributed to oxidized Mn that acted as a temporary redox buffer in the pristine sediment. The oxidized Mn was transformed to Mn(II) during bioreduction but, unlike silicate Fe(II), was not re-oxidized when exposed to oxygen.

Oxidative remobilization of biogenic uranium(IV) precipitates: effects of iron(II) and pH.

The oxidative remobilization of uranium from biogenic U(IV) precipitates was investigated in bioreduced sediment suspensions in contact with atmospheric O2 with an emphasis on the influence of Fe(II) and pH on the rate and extent of U release from the solid to the aqueous phase. The sediment was collected from the U.S. Department of Energy Field Research Center (FRC) site at Oak Ridge, Tennessee. Biogenic U(IV) precipitates and bioreduced sediment were generated through anaerobic incubation with a dissimilatory metal reducing bacterium Shewanella putrefaciens strain CN32. The oxidative remobilization of freshly prepared and 1-yr aged biogenic U(IV) was conducted in 0.1 mol/L NaNO3 electrolyte with variable pH and Fe(II) concentrations. Biogenic U(IV)O2(s) was released into the aqueous phase with the highest rate and extent at pH 4 and 9, while the U remobilization was the lowest at circumneutral pH. Increasing Fe(II) significantly decreased U remobilization to the aqueous phase. From 70 to 100% of the U in the sediments used in all the tests was extractable at the experiment termination (41 d) with a bicarbonate solution (0.2 mol/L), indicating that biogenic U(IV) was oxidized regardless of Fe(II) concentration and pH. Sorption experiments and modeling calculations indicated that the inhibitive effect of Fe(II) on U(IV) oxidative remobilization was consistent with the Fe(III) oxide precipitation and U(VI) sorption to this secondary phase.